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ORCIDPaul T. Spellman
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Journal Articles
- 2023
[j21]Tao Ren
, Canping Chen, Alexey V. Danilov, Susan Liu, Xiangnan Guan, Shunyi Du, Xiwei Wu, Mara H. Sherman, Paul T. Spellman, Lisa M. Coussens, Andrew C. Adey, Gordon B. Mills, Ling-Yun Wu, Zheng Xia:
Supervised learning of high-confidence phenotypic subpopulations from single-cell data. Nat. Mac. Intell. 5(5): 528-541 (2023)- [j20]Tao Ren, Canping Chen, Alexey V. Danilov, Susan Liu, Xiangnan Guan, Shunyi Du, Xiwei Wu, Mara H. Sherman, Paul T. Spellman, Lisa M. Coussens, Andrew C. Adey, Gordon B. Mills, Ling-Yun Wu, Zheng Xia:
Author Correction: Supervised learning of high-confidence phenotypic subpopulations from single-cell data. Nat. Mac. Intell. 5(6): 676 (2023) - 2021
- [j19]Özgün Babur, Augustin Luna, Anil Korkut, Funda Durupinar, Metin Can Siper, Ugur Dogrusoz, Alvaro Sebastian Vaca Jacome, Ryan Peckner, Karen E. Christianson, Jacob D. Jaffe, Paul T. Spellman, Joseph E. Aslan, Chris Sander, Emek Demir:
Causal interactions from proteomic profiles: Molecular data meet pathway knowledge. Patterns 2(6): 100257 (2021) - 2020
- [j18]Moritz Gerstung, Clemency Jolly, Ignaty Leshchiner, Stefan C. Dentro, Santiago Gonzalez, Thomas J. Mitchell, Yulia Rubanova, Pavana Anur, Kaixian Yu, Maxime Tarabichi, Amit G. Deshwar, Jeff Wintersinger, Kortine Kleinheinz, Ignacio Vázquez-García, Kerstin Haase, Lara Jerman, Subhajit Sengupta, Geoff MacIntyre, Salem Malikic, Nilgun Donmez, Dimitri G. Livitz, Marek Cmero, Jonas Demeulemeester, Steven E. Schumacher, Yu Fan, Xiaotong Yao, Juhee Lee, Matthias Schlesner, Paul C. Boutros, David D. L. Bowtell, Hongtu Zhu, Gad Getz, Marcin Imielinski, Rameen Beroukhim, Süleyman Cenk Sahinalp, Yuan Ji, Martin Peifer, Florian Markowetz, Ville Mustonen, Ke Yuan, Wenyi Wang, Quaid D. Morris, David J. Adams, Peter J. Campbell, Shaolong Cao, Elizabeth L. Christie, Yupeng Cun, Kevin J. Dawson, Ruben M. Drews, Roland Eils, Matthew Fittall, Dale W. Garsed, Gavin Ha, Henry Lee-Six, Iñigo Martincorena, Layla Oesper, Myron Peto, Benjamin J. Raphael, Daniel T. Rosebrock, Adriana Salcedo, Ruian Shi, Seung Jun Shin, Oliver Spiro, Lincoln D. Stein, Shankar Vembu, David A. Wheeler, Tsun-Po Yang, Paul T. Spellman, David C. Wedge, Peter Van Loo:
The evolutionary history of 2,658 cancers. Nat. 578(7793): 122-128 (2020) - 2015
- [j17]Hang Chang, Yin Zhou, Alexander Borowsky, Kenneth E. Barner, Paul T. Spellman, Bahram Parvin:
Stacked Predictive Sparse Decomposition for Classification of Histology Sections. Int. J. Comput. Vis. 113(1): 3-18 (2015) - 2013
- [j16]Elizabeth Purdom, Christine Ho, Catherine S. Grasso, Michael Quist, Raymond J. Cho, Paul T. Spellman:
Methods and challenges in timing chromosomal abnormalities within cancer samples. Bioinform. 29(24): 3113-3120 (2013) - [j15]Hang Chang, Ju Han, Alexander Borowsky, Leandro A. Loss, Joe W. Gray, Paul T. Spellman, Bahram Parvin:
Invariant Delineation of Nuclear Architecture in Glioblastoma Multiforme for Clinical and Molecular Association. IEEE Trans. Medical Imaging 32(4): 670-682 (2013) - 2012
- [j14]Steven M. Hill, Yiling Lu, Jennifer Molina, Laura Heiser, Paul T. Spellman, Terence P. Speed, Joe W. Gray, Gordon B. Mills, Sach Mukherjee:
Bayesian Inference of Signaling Network Topology in a Cancer Cell Line. Bioinform. 28(21): 2804-2810 (2012) - [j13]Steven M. Hill, Richard M. Neve, Nora Bayani, Wen-Lin Kuo, Safiyyah Ziyad, Paul T. Spellman, Joe W. Gray, Sach Mukherjee:
Integrating biological knowledge into variable selection: an empirical Bayes approach with an application in cancer biology. BMC Bioinform. 13: 94 (2012) - [j12]Hang Chang, Ju Han, Paul T. Spellman, Bahram Parvin:
Multireference Level Set for the Characterization of Nuclear Morphology in Glioblastoma Multiforme. IEEE Trans. Biomed. Eng. 59(12): 3460-3467 (2012) - 2011
- [j11]Adam B. Olshen, Henrik Bengtsson, Pierre Neuvial, Paul T. Spellman, Richard A. Olshen, Venkatraman E. Seshan:
Parent-specific copy number in paired tumor-normal studies using circular binary segmentation. Bioinform. 27(15): 2038-2046 (2011) - [j10]Hang Chang, Gerald Fontenay, Ju Han, Ge Cong, Frederick L. Baehner, Joe W. Gray, Paul T. Spellman, Bahram Parvin:
Morphometic analysis of TCGA glioblastoma multiforme. BMC Bioinform. 12: 484 (2011) - 2010
- [j9]Leandro A. Loss, Anguraj Sadanandam, Steffen Durinck, Shivani Nautiya, Diane Flaucher, Victoria E. H. Carlton, Martin Moorhead, Yontao Lu, Joe W. Gray, Malek Faham, Paul T. Spellman, Bahram Parvin:
Prediction of epigenetically regulated genes in breast cancer cell lines. BMC Bioinform. 11: 305 (2010) - 2009
- [j8]Sach Mukherjee, Steven Pelech, Richard M. Neve, Wen-Lin Kuo, Safiyyah Ziyad, Paul T. Spellman, Joe W. Gray, Terence P. Speed:
Sparse combinatorial inference with an application in cancer biology. Bioinform. 25(2): 265-271 (2009) - [j7]Henrik Bengtsson, Amrita Ray, Paul T. Spellman, Terence P. Speed:
A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods. Bioinform. 25(7): 861-867 (2009) - [j6]Steffen Durinck, James H. Bullard, Paul T. Spellman, Sandrine Dudoit:
GenomeGraphs: integrated genomic data visualization with R. BMC Bioinform. 10 (2009) - 2006
- [j5]Tim F. Rayner, Philippe Rocca-Serra, Paul T. Spellman, Helen C. Causton, Anna Farne, Ele Holloway, Rafael A. Irizarry, Junmin Liu, Donald Maier, Michael Miller, Kjell Petersen, John Quackenbush, Gavin Sherlock, Christian J. Stoeckert Jr., Joseph White, Patricia L. Whetzel, Farrell Wymore, Helen E. Parkinson, Ugis Sarkans, Catherine A. Ball, Alvis Brazma:
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinform. 7: 489 (2006) - 2005
- [j4]Paul T. Spellman:
A Status Report on Mage. Bioinform. 21(17): 3459-3460 (2005) - 2002
- [j3]Catherine A. Ball, Gavin Sherlock, Helen E. Parkinson, Philippe Rocca-Serra, Catherine Brooksbank, Helen C. Causton, Duccio Cavalieri, Terry Gaasterland, Pascal Hingamp, Frank C. P. Holstege, Martin Ringwald, Paul T. Spellman, Christian J. Stoeckert Jr., Jason E. Stewart, Ronald C. Taylor, Alvis Brazma, John Quackenbush:
An open letter to the scientific journals. Bioinform. 18(11): 1409 (2002) - 2001
- [j2]Paul T. Spellman:
Editorial: The Future of Publishing Microarray Data. Briefings Bioinform. 2(4): 316-318 (2001) - [j1]Gavin Sherlock, Tina Hernandez-Boussard, Andrew Kasarskis, Gail Binkley, John C. Matese, Selina S. Dwight, Miroslava Kaloper, Shuai Weng, Heng Jin, Catherine A. Ball, Michael B. Eisen, Paul T. Spellman, Patrick O. Brown, David Botstein, J. Michael Cherry:
The Stanford Microarray Database. Nucleic Acids Res. 29(1): 152-155 (2001)
Conference and Workshop Papers
- 2015
- [c12]Hang Chang, Paul T. Spellman, Bahram Parvin:
Predictive sparse morphometric context for classification of histology sections. ISBI 2015: 1004-1007 - 2014
- [c11]Yin Zhou, Hang Chang, Kenneth E. Barner, Paul T. Spellman, Bahram Parvin:
Classification of Histology Sections via Multispectral Convolutional Sparse Coding. CVPR 2014: 3081-3088 - 2013
- [c10]Hang Chang, Alexander Borowsky, Paul T. Spellman, Bahram Parvin:
Classification of Tumor Histology via Morphometric Context. CVPR 2013: 2203-2210 - [c9]Hang Chang, Yin Zhou, Paul T. Spellman, Bahram Parvin:
Stacked Predictive Sparse Coding for Classification of Distinct Regions in Tumor Histopathology. ICCV 2013: 169-176 - [c8]Nandita Nayak, Hang Chang, Alexander Borowsky, Paul T. Spellman, Bahram Parvin:
Classification of tumor histopathology via sparse feature learning. ISBI 2013: 410-413 - [c7]Nandita Nayak, Hang Chang, Alexander Borowsky, Paul T. Spellman, Bahram Parvin:
Classification of tumor histopathology via sparse feature learning. ISBI 2013: 1348-1351 - [c6]Hang Chang, Nandita Nayak, Paul T. Spellman, Bahram Parvin:
Characterization of Tissue Histopathology via Predictive Sparse Decomposition and Spatial Pyramid Matching. MICCAI (2) 2013: 91-98 - 2012
- [c5]Quoc V. Le, Ju Han, Joe W. Gray, Paul T. Spellman, Alexander Borowsky, Bahram Parvin:
Learning invariant features of tumor signatures. ISBI 2012: 302-305 - [c4]Hang Chang, Leandro A. Loss, Paul T. Spellman, Alexander Borowsky, Bahram Parvin:
Batch-invariant nuclear segmentation in whole mount histology sections. ISBI 2012: 856-859 - [c3]Ju Han, Hang Chang, Gerald Fontenay, Paul T. Spellman, Alexander Borowsky, Bahram Parvin:
Molecular bases of morphometric composition in Glioblastoma multiforme. ISBI 2012: 1631-1634 - 2011
- [c2]Ju Han, Hang Chang, Leandro A. Loss, Kai Zhang, Frederick L. Baehner, Joe W. Gray, Paul T. Spellman, Bahram Parvin:
Comparison of sparse coding and kernel methods for histopathological classification of gliobastoma multiforme. ISBI 2011: 711-714 - 2007
- [c1]Bahram Parvin, Nirmalya Ghosh, Laura Heiser, Merrill Knapp, Carolyn L. Talcott, Keith Laderoute, Joe W. Gray, Paul T. Spellman:
Spectral Decomposition of Signaling Networks. CIBCB 2007: 76-81
Coauthor Index
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